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1.  A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i) 
BMC Bioinformatics  2014;15:111.
Background
Small insertion and deletion polymorphisms (Indels) are the second most common mutations in the human genome, after Single Nucleotide Polymorphisms (SNPs). Recent studies have shown that they have significant influence on genetic variation by altering human traits and can cause multiple human diseases. In particular, many Indels that occur in protein coding regions are known to impact the structure or function of the protein. A major challenge is to predict the effects of these Indels and to distinguish between deleterious and neutral variants. When an Indel occurs within a coding region, it can be either frameshifting (FS) or non-frameshifting (NFS). FS-Indels either modify the complete C-terminal region of the protein or result in premature termination of translation. NFS-Indels insert/delete multiples of three nucleotides leading to the insertion/deletion of one or more amino acids.
Results
In order to study the relationships between NFS-Indels and Mendelian diseases, we characterized NFS-Indels according to numerous structural, functional and evolutionary parameters. We then used these parameters to identify specific characteristics of disease-causing and neutral NFS-Indels. Finally, we developed a new machine learning approach, KD4i, that can be used to predict the phenotypic effects of NFS-Indels.
Conclusions
We demonstrate in a large-scale evaluation that the accuracy of KD4i is comparable to existing state-of-the-art methods. However, a major advantage of our approach is that we also provide the reasons for the predictions, in the form of a set of rules. The rules are interpretable by non-expert humans and they thus represent new knowledge about the relationships between the genotype and phenotypes of NFS-Indels and the causative molecular perturbations that result in the disease.
doi:10.1186/1471-2105-15-111
PMCID: PMC4021375  PMID: 24742296
Genotype-phenotype relationship; Insertion/deletion; Machine learning; Indeuctive logic programming
2.  Identification and Characterization of Two Novel Viruses in Ocular Infections in Reindeer 
PLoS ONE  2013;8(7):e69711.
A thorough understanding of virus diversity in wildlife provides epidemiological baseline information about pathogens. In this study, eye swab samples were obtained from semi-domesticated reindeer (Rangifertarandustarandus) in Norway during an outbreak of infectious eye disease, possibly a very early stage of infectious keratoconjunctivitis (IKC). Large scale molecular virus screening, based on host nucleic acid depletion, sequence-independent amplification and next-generation sequencing of partially purified viral nucleic acid, revealed the presence of a new papillomavirus in 2 out of 8 eye swab samples and a new betaherpesvirus in 3 out of 8 eye swab samples collected from animals with clinical signs and not in similar samples in 9 animals without clinical signs. Whether either virus was responsible for causing the clinical signs or in any respect was associated to the disease condition remains to be determined.
doi:10.1371/journal.pone.0069711
PMCID: PMC3713034  PMID: 23874987
3.  OME Remote Objects (OMERO): a flexible, model-driven data management system for experimental biology 
Nature methods  2012;9(3):245-253.
Data-intensive research depends on tools that manage multi-dimensional, heterogeneous data sets. We have built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices, and tables. OMERO’s design and flexibility have enabled its use for light microscopy, high content screening, electron microscopy, and even non-image genotype data. OMERO is open source software and available at http://openmicroscopy.org.
doi:10.1038/nmeth.1896
PMCID: PMC3437820  PMID: 22373911
4.  Tissue specific characterisation of Lim-kinase 1 expression during mouse embryogenesis 
Gene expression patterns : GEP  2010;11(3-4):221-232.
The Lim-kinase (LIMK) proteins are important for the regulation of the actin cytoskeleton, in particular the control of actin nucleation and depolymerisation via regulation of cofilin, and hence may control a large number of processes during development, including cell tensegrity, migration, cell cycling, and axon guidance. LIMK1/LIMK2 knockouts disrupt spinal cord morphogenesis and synapse formation but other tissues and developmental processes that require LIMK are yet to be fully determined. To identify tissues and cell-types that may require LIMK, we characterised the pattern of LIMK1 protein during mouse embryogenesis. We showed that LIMK1 displays an expression pattern that is temporally dynamic and tissue-specific. In several tissues LIMK1 is detected in cell-types that also express Wilms’ tumour protein 1 and that undergo transitions between epithelial and mesenchymal states, including the pleura, epicardium, kidney nephrons, and gonads. LIMK1 was also found in a subset of cells in the dorsal retina, and in mesenchymal cells surrounding the peripheral nerves. This detailed study of the spatial and temporal expression of LIMK1 shows that LIMK1 expression is more dynamic than previously reported, in particular at sites of tissue–tissue interactions guiding multiple developmental processes.
doi:10.1016/j.gep.2010.12.003
PMCID: PMC3407955  PMID: 21167960
Limk; Kidney; Heart; Epithelia-to-mesenchyme transition; Mesenchyme-to-epithelia transition; Eye; Testes
5.  Modulation of Vasomotive Activity in Rabbit External Ophthalmic Artery by Neuropeptides 
Journal of Ophthalmology  2012;2012:498565.
Purpose. To investigate the vasomotive activity upon the external ophthalmic artery of vasointestinal peptide (VIP) and neuropeptide Y (NPY) using a previously developed model. Methods. Isolated rabbit eyes (n = 12) were perfused in situ with tyrode through the external ophthalmic artery. Effects of intra-arterial injections of NPY 200 μg/ml (Group A; n = 6) and VIP 200 μg/ml (Group B; n = 6) on the recorded pressure were obtained. For statistical analysis, Student's paired t-test and Fast Fourier Transform were used. Results. Spontaneous oscillations were observed before any drug administration in the 12 rabbit models. NPY produced an increase in total vascular resistance and a higher frequency and amplitude of oscillations, while VIP evoked the opposite effects. Conclusions. This study provides evidence of vasomotion in basal conditions in rabbit external ophthalmic artery. Concerning drug effects, NPY increased arterial resistance and enhanced vasomotion while VIP produced opposite effects which demonstrates their profound influence in arterial vasomotion.
doi:10.1155/2012/498565
PMCID: PMC3306996  PMID: 22496962
6.  Evidence of alphaherpesvirus infections in Alaskan caribou and reindeer 
Background
The reindeer (Rangifer tarandus tarandus) industry in Alaska began with animals imported from Siberia (Russia) in the 1890's. Cervid herpes virus 2 (CvHV2) is endemic in reindeer in Scandinavia. We sought to determine if the same virus, or similar herpesviruses, were circulating in Alaskan reindeer and caribou (Rangifer tarandus granti). Serum samples from 292 reindeer were collected during annual reindeer handlings (1988-2005) near Nome, Alaska. In 2005, swab samples were collected from 40 calves from this herd, near Nome, Alaska. In 2007, ocular and nasal swab samples were collected from 30 apparently healthy reindeer calves near Wales, Alaska. Samples of plasma and white blood cells were collected from three Alaskan caribou herds, Mulchatna (n = 24), Teshekpuk (n = 34) and the Western Arctic (n = 87) in 2009.
Results
Of 292 reindeer samples tested by ELISA for antibodies against alphaherpesvirus (bovine herpesvirus 1 as antigen), seroprevalence was 47% (136/292) and adult reindeer had higher seroprevalence than yearlings. The overall seroprevalence for caribou was 60% (87/145), with no significant differences among caribou herds. A virus neutralization test of 20 samples from both reindeer and caribou showed that ELISA positive samples always neutralized CvHV2 to a greater extent than BoHV1 or elk herpesvirus (ElkHV), indicating that CvHv2 is the most likely virus circulating. PCR of nasal and ocular swabs sampled from 30 reindeer calves in Wales, Alaska (2007) yielded four CvHV2 positive samples. PCR amplicons of the expected size (294 bp) were obtained from 2 of the 36 buffy coats samples from caribou, and the amplicon sequences were consistent with CvHV2.
Conclusions
This study shows that Alaskan reindeer and Caribou are infected with an alphaherpesvirus. Based on sequence similarity, CvHV-2 is the most likely virus. Further studies should be conducted to determine the impact of this infection on the health of these animals.
doi:10.1186/1746-6148-8-5
PMCID: PMC3274481  PMID: 22243919
caribou; epidemiology; herd health; herpesvirus infectious diseases; reindeer; Rangifer; wildlife medicine
7.  Interaction between hedgehog signalling and PAX6 dosage mediates maintenance and regeneration of the corneal epithelium 
Molecular Vision  2012;18:139-150.
Purpose
To investigate the roles of intracellular signaling elicited by Hedgehog (Hh) ligands in corneal maintenance and wound healing.
Methods
The expression of Hedgehog pathway components in the cornea was assayed by immunohistochemistry, western blot and reverse-transcription polymerase chain reaction (RT-PCR), in wild-type mice and mice that were heterozygous null for the gene encoding the transcription factor, paired box gene 6 (Pax6).  Corneal epithelial wound healing and cell migration assays were performed after pharmacological upregulation and downregulation of the hedgehog pathway.  Reporter mice, mosaic for expression of the gene encoding β-galactosidase (LacZ), were crossed to Pax6+/- mice, mice heterozygous for the gene encoding GLI-Kruppel family member GLI3, and Pax6+/- Gli3+/- double heterozygotes, to assay patterns of cell migration and corneal epithelial organization in vivo.
Results
Corneal epithelial wound healing rates increased in response to application of Sonic hedgehog (Shh), but only in mice with wild-type Pax6 dosage.  Downregulation of Hedgehog signalling inhibited corneal epithelial cell proliferation.  Pax6+/- corneal epithelia showed increased proliferation in response to exogenous Shh, but not increased migration. Desert hedgehog (Dhh) was shown to be the major endogenous ligand, with Shh detectable only by RT-PCR and only after epithelial wounding. The activity of phosphatidylinositol-3-OH kinase-γ (PI3Kγ) was not required for the increased migration response in response to Shh.  Nuclear expression of the activator form of the transcription factor Gli3 (which mediates Hh signalling) was reduced in Pax6+/- corneal epithelia. Pax6+/- Gli3+/- double heterozygotes showed highly disrupted patterns of clonal arrangement of cells in the corneal epithelium.
Conclusions
The data show key roles for endogenous Dhh signalling in maintenance and regeneration of the corneal epithelium, demonstrate an interaction between Pax6 and Hh signalling in the corneal epithelium, and show that failure of Hh signalling pathways is a feature of Pax6+/- corneal disease that cannot be remedied pharmacologically by addition of the ligands.
PMCID: PMC3265179  PMID: 22275805
8.  Metadata matters: access to image data in the real world 
The Journal of Cell Biology  2010;189(5):777-782.
Data sharing is important in the biological sciences to prevent duplication of effort, to promote scientific integrity, and to facilitate and disseminate scientific discovery. Sharing requires centralized repositories, and submission to and utility of these resources require common data formats. This is particularly challenging for multidimensional microscopy image data, which are acquired from a variety of platforms with a myriad of proprietary file formats (PFFs). In this paper, we describe an open standard format that we have developed for microscopy image data. We call on the community to use open image data standards and to insist that all imaging platforms support these file formats. This will build the foundation for an open image data repository.
doi:10.1083/jcb.201004104
PMCID: PMC2878938  PMID: 20513764
9.  Experimental Infection of Reindeer with Cervid Herpesvirus 2▿  
Clinical and Vaccine Immunology : CVI  2009;16(12):1758-1765.
Cervid herpesvirus 2 (CvHV2) has been isolated from reindeer (Rangifer tarandus tarandus), and serological data indicate that in reindeer this virus is endemic in Fennoscandia, Alaska, Canada, and Greenland. CvHV2 has been described as a cause of subclinical genital infections in reindeer, but little information on primary infections exists. In this study, six seronegative and presumably pregnant reindeer were allocated to one of two groups. Two animals were inoculated with CvHV2 intratracheally, and two animals intravaginally, with one control animal in each group receiving sterile water. Mild hyperthermia and serous discharges from the vagina and nose were observed. No abortions were recorded, but one calf died shortly after birth. Inoculated animals seroconverted and had neutralizing antibodies after days 7 to 10 postinfection. CvHV2 was detected by PCR in nasal and vaginal swabs from animals in both groups but could be isolated only from nasal swabs in the respiratory group and from vaginal swabs in the genital group. CvHV2 was detected by PCR in various organs and tissues postmortem. In control animals, the virus could not be isolated in spite of PCR-positive nasal and vaginal swab samples and some degree of positive immunostaining. One of the animals that were inoculated intratracheally developed a hemorrhagic, necrotizing bronchopneumonia, which was CvHV2 positive by PCR and immunohistochemistry. We conclude that CvHV2 can cause systemic infection, that both genital and respiratory inoculations can lead to virus shedding, and that the virus can infect the fetus in utero.
doi:10.1128/CVI.00218-09
PMCID: PMC2786388  PMID: 19846680
10.  Cervid Herpesvirus 2, the Primary Agent in an Outbreak of Infectious Keratoconjunctivitis in Semidomesticated Reindeer ▿  
Journal of Clinical Microbiology  2009;47(11):3707-3713.
An outbreak of infectious keratoconjunctivitis (IKC) occurred in semidomesticated reindeer (Rangifer tarandus tarandus) in Troms County, Norway, in February 2009. Twenty-eight animals with clinical symptoms and 12 apparently healthy animals were investigated. They ranged in age from calves of the year to 4-year-old animals (mean, 1.9 years; standard deviation, ±0.9). The seroprevalence of antibodies against cervid herpesvirus 2 (CvHV2) was 86% in animals with IKC and 42% in unaffected animals. For the 28 clinically affected animals, CvHV2 was detected by PCR in swabs obtained from the eye (82%), nose (64%), and vagina (24%), and CvHV2 was isolated from eye swabs from 8 animals. Virus was not isolated from clinically unaffected animals but was detected by PCR in eye swab samples from five of them. The viral activity, assessed by the ability to cause a cytopathic effect in cell culture, increased with the severity of clinical symptoms, but in severe clinical cases, virus was absent and secondary bacterial infections were dominant. Moraxella sp. isolates were obtained from seven animals, and those from two animals were identified as Moraxella bovoculi. Staphylococcus aureus, Streptococcus sp., and Arcanobacterium pyogenes were also isolated. It is concluded that CvHV2, which is endemic in reindeer, can cause IKC, probably most commonly as a primary infection of calves. This can be a very painful and devastating disease of economic importance for reindeer herders. This is the first report of CvHV2 as the primary agent of IKC in reindeer. This is also the first isolation of this virus in reindeer under natural herding conditions.
doi:10.1128/JCM.01198-09
PMCID: PMC2772613  PMID: 19726598
11.  Cervid Herpesvirus 2 Causes Respiratory and Fetal Infections in Semidomesticated Reindeer▿  
Journal of Clinical Microbiology  2009;47(5):1309-1313.
Members of the viral subfamily Alphaherpesvirinae establish latency from which they can be reactivated. Bovine herpesvirus 1 causes infectious bovine rhinotracheitis and infectious pustular vulvovaginitis in cattle, as well as abortion and weak calves. Serological evidence of alphaherpesvirus infection has been reported for wild and semidomesticated reindeer (Rangifer tarandus tarandus) in Norway. To address the possibility that reindeer alphaherpesvirus (cervid herpesvirus 2 [CvHV-2]) infection might affect the respiratory system and in part explain the relatively high mortality of reindeer calves during their first year, tissue samples were obtained from reindeer and reindeer fetuses at slaughterhouses in Finnmark County, Norway. A nested pan-alphaherpesvirus PCR amplification targeting the highly conserved UL27 gene (encoding glycoprotein B) was used. Sequencing of amplicons revealed the presence of CvHV-2 DNA. The detection of CvHV-2 DNA in trigeminal ganglia (27 of 143 samples), nasal swabs (5 of 75 samples), and fetal tissues (12 of 48 samples) indicates that CvHV-2 infection is endemic in this reindeer population. Moreover, the virus is transmitted horizontally by the respiratory route, establishing latency in the trigeminal ganglion, and vertically to the fetus through the placenta. Further studies should focus on the reproductive impact of CvHV-2 infection in reindeer.
doi:10.1128/JCM.02416-08
PMCID: PMC2681864  PMID: 19279181
12.  Evaluation of three commercial bovine ELISA kits for detection of antibodies against Alphaherpesviruses in reindeer (Rangifer tarandus tarandus) 
Background
The genus Varicellovirus (family Herpesviridae subfamily Alphaherpesvirinae) includes a group of viruses genetically and antigenically related to bovine herpesvirus 1 (BoHV-1) among which cervid herpesvirus 2 (CvHV-2) can be of importance in reindeer. These viruses are known to be responsible for different diseases in both wild and domestic animals. Reindeer are a keystone in the indigenous Saami culture and previous studies have reported the presence of antibodies against alphaherpesviruses in semi-domesticated reindeer in northern Norway. Mortality rates, especially in calves, can be very high in some herds and the abortion potential of alphaherpesvirus in reindeer, unlike in bovines, remains unknown.
ELISA kits are the most used screening method in domestic ruminants and given the close genetic relationship between viruses within this genus, it might be possible to use such kits to screen cervids for different alphaherpesviruses. We have compared three different commercial ELISA kits in order to validate its use for reindeer and CvHV-2.
Methods
Three commercial bovine ELISA kits (A, B and C), using either indirect (A) or blocking (B and C) ELISA techniques to detect antibodies against BoHV-1 were tested with sera from 154 reindeer in order to detect antibodies against CvHV-2. A Spearman's rank-based coefficient of correlation (ρ) was calculated. A dilution trial was performed for all kits. A virus neutralization test using both BoHV-1 and CvHV-2 was carried out.
Results
Seroprevalence was almost the same with all kits (40–41%). Despite a similar qualitative score, quantitatively kits classified samples differently and a strong correlation was only identified between Kits B and C. Blocking kits performed better in both repeatability and in the dilution trial. The virus neutralization results confirmed the ELISA results to a very high degree. Neutralizing titres ranged from 1:2 to 1:256 and from 0 to 1:16 against CvHV-2 and BoHV-1 respectively.
Conclusion
Results show that the genetic and antigenic similarity between BoHV-1 and CvHV-2 enables the use of a bovine gB blocking ELISA kit to screen reindeer. The use of an ELISA kit is both cheaper and time saving, allowing screening of large populations. This study revealed a high number of positive animals against CvHV-2 and its impact and distribution in the general population should be further evaluated.
doi:10.1186/1751-0147-51-9
PMCID: PMC2663558  PMID: 19272136

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